Alignments for a candidate for tpi in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Pseudomonas fluorescens GW456-L13

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate PfGW456L13_5091 Triosephosphate isomerase (EC 5.3.1.1)

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091
          Length = 247

 Score =  231 bits (589), Expect = 1e-65
 Identities = 123/246 (50%), Positives = 163/246 (66%), Gaps = 2/246 (0%)

Query: 5   LVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQ 64
           +V GNWK++G+R  V EL++ LR +LA  +   VA+ PP ++I+      EG  I +GAQ
Sbjct: 1   MVAGNWKMHGTRASVAELINGLR-DLALPSSVDVAVFPPFLHINQVIEGLEGKSISVGAQ 59

Query: 65  NVDLNLS-GAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTP 123
           N  +    GA TGE + + L D G   +++GHSERR    E D ++ +KFA  +  GLTP
Sbjct: 60  NSAVESGQGALTGEVAPSQLVDAGCSLVLVGHSERRQILGEQDAVLIRKFAAAQACGLTP 119

Query: 124 VLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQA 183
           VLCIGET  + EAGKT EV +RQ+ ++++  G  AF  AVIAYEPVWAIGTG +ATP QA
Sbjct: 120 VLCIGETLEQREAGKTLEVVSRQLGSIIEELGVGAFAKAVIAYEPVWAIGTGLTATPQQA 179

Query: 184 QAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFA 243
           Q VH  IR  +A  ++ +A+ V + YGGSV A+NA ELF  PDIDG L+GGASL AD F 
Sbjct: 180 QDVHAAIRAQLAAENSEVAQGVRLLYGGSVKAANAVELFGMPDIDGGLIGGASLNADEFG 239

Query: 244 VIVKAA 249
            I +AA
Sbjct: 240 AICRAA 245


Lambda     K      H
   0.316    0.130    0.366 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 187
Number of extensions: 9
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 255
Length of database: 247
Length adjustment: 24
Effective length of query: 231
Effective length of database: 223
Effective search space:    51513
Effective search space used:    51513
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 bits)

Align candidate PfGW456L13_5091 (Triosephosphate isomerase (EC 5.3.1.1))
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00419.hmm
# target sequence database:        /tmp/gapView.28321.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00419  [M=228]
Accession:   TIGR00419
Description: tim: triose-phosphate isomerase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
    1.5e-67  213.7   1.4    1.7e-67  213.5   1.4    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091  Triosephosphate isomerase (EC 5.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091  Triosephosphate isomerase (EC 5.3.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.5   1.4   1.7e-67   1.7e-67       1     228 []       1     236 [.       1     236 [. 0.95

  Alignments for each domain:
  == domain 1  score: 213.5 bits;  conditional E-value: 1.7e-67
                                               TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.sei 54 
                                                             +v +n+K+++++ +v+++++ l+ ++a ++ v vav ppf++++ v + +e   i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091   1 MVAGNWKMHGTRASVAELINGLR-DLALPSSVDVAVFPPFLHINQVIEGLEgKSI 54 
                                                             699******************97.79*************************999* PP

                                               TIGR00419  55 qvaAqnvdav.ksGaftGeisAemlkdlGakgvligHsErRsllkeadeliekkv 108
                                                             +v+Aqn  +   +Ga tGe+    l+d+G+  vl+gHsErR +l e d ++  k+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091  55 SVGAQNSAVEsGQGALTGEVAPSQLVDAGCSLVLVGHSERRQILGEQDAVLIRKF 109
                                                             ******9986257****************************************** PP

                                               TIGR00419 109 arlkelglksvvCvgetleereaartinnvattaaaaA.......lepdvvAvEP 156
                                                             a +++ gl++v+C+getle+rea++t+++v ++ + +        + ++v+A+EP
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091 110 AAAQACGLTPVLCIGETLEQREAGKTLEVVSRQLGSIIeelgvgaFAKAVIAYEP 164
                                                             **********************99999999888877766666666********** PP

                                               TIGR00419 157 veliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaa 211
                                                             v++iGtG ++++ +a+ v++ +r  l+  + eva+ vr+lyG+sv+aa+++el+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091 165 VWAIGTGLTATPQQAQDVHAAIRAQLAAENSEVAQGVRLLYGGSVKAANAVELFG 219
                                                             ******************************************************* PP

                                               TIGR00419 212 qldvdGvLlasavlkae 228
                                                              +d+dG L+++a+l a+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091 220 MPDIDGGLIGGASLNAD 236
                                                             **************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (247 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.19
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources